Litbium intercalated bilayer graphene has been investigated using first-principles density functional theory calculations. Re- sults show that there exist AB and AA stacking sequences for bilayer graphene in which the latter is more favorable for the Li storage and the former will evolve into the latter with the intercalation of Li ions. The relationship between the interlayer dis- tance of two graphene sheets and the intercalated capacity of Li ions is discussed, It is found that structural defect is identified to store Li ions more favorably than pristine bilayer graphene and an isolated C atom vacancy in bilayer graphene can capture three Li ions between two graphene sheets.